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CHAPTER FIVE
PAPER THREE
JERE, K. C., MLERA, L., O'NEILL, H. G., PEENZE, I. & VAN DIJK, A. A. 2011. Whole
genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species.
Vet Microbiol, In press, Accepted Manuscript, Available online 6 April 2012. http://dx.doi.org/10.1016/j.vetmic.2012.03.040
Instructions to the authors for this journal may be found at the following website:
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Supplementary Data
Supplement 1: Accession numbers of the complete consensus nucleotide and amino acid sequences of the three African
bovine rotaviruses analysed in this study.
Study bovine rotaviruses GenBank accession numbers
S9(VP7) S4(VP4) S6(VP6) S1(VP1) S2(VP2) S3(VP3) S5(NSP1) S8(NSP2) S7(NSP3) S10(NSP4) S11(NSP5) RVA/Cow-wt/ZAF/1603/2007/G6P[5] JN831209 JN831210 JN831211 JN831212 JN831213 JN831214 JN831204 JN831205 JN831206 JN831207 JN831208 RVA/Cow-wt/ZAF/1604/2007/G8P[1] JN831220 JN831221 JN831222 JN831223 JN831224 JN831225 JN831215 JN831216 JN831217 JN831218 JN831219 RVA/Cow-wt/ZAF/1605/2007/G6P[5] JN831231 JN831232 JN831233 JN831234 JN831235 JN831236 JN831226 JN831227 JN831228 JN831229 JN831230
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Supplement 2:
Accession numbers for the selected nucleotide
sequences acquired from the GenBank.
Genome segment 1 (VP1)
RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495126; RVA/Human-wt/KEN/B12/1987/ G8P[1]: HM627542; RVA/Cow-tc/FRA/RF/1982/G6P[1]: J04346; RVA/USA/Rotashield-ST3xRRV/XXXX/G4P[3]: HQ846876; RVA/Vaccine/USA/RotaTeq-WI79-4/1992/ G6P1A[8]: GU565041; tc/USA/Se584/1998/G6P[9]: EF583041; RVA/Human-wt/ITA/PAI58/1996/G3P[9]: GU296421; RVA/Human-tc/AUS/MG6/1993/G6P[14]: EF554093; RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF560615; RVA/Cow-tc/VEN/BRV033/ 1990/G6P6[1]: EF560612; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009629; RVA/Human-tc/USA/DS-1/1976/G2P[4]: HQ650116; RVA/Human-wt/ZAF/3203WC/ 2009/G2P[4]: HQ657166; RVA/Human-wt/ZAF/GR10924/1999/ G9P[6]: FJ183353; RVA/Human-wt/MWI/1473/2001/G8P[4: HQ657133; RVA/Human-wt/COD/DRC86/2003/ G8P[6]: DQ005125; wt/COD/DRC88/2003/G8P[8]: DQ005114; RVA/Human-wt/USA/ LB2764/2006/G2P[4]: HM467926; RVA/Human-wt/CHN/TB-Chen/1996/G2P[4]: AY78765.
Genome segment 2 (VP2)
RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495127; RVA/Human-wt/ITA/ PAH136/ 1996/G3P[9]: GU296422; RVA/Human-wt/HUN/Hun5/1997/G6P[14]: EF554105; RVA/Human-wt/EGY/Egy3399/2004/G6P[14]: HM113526; RVA/Human-wt/BGD/ RV176/2000/G12P[6]: DQ490552; RVA/giraffe/IRL/UCD/2007/G10P[11]: GQ428142; RVA/Human-tc/JPN/S2/1980/G2P1B[4]: DQ870486; RVA/Human-tc/USA/DS-1/1976/ G2P1B[4]: DQ870506; RVA/Human-wt/CHN/TB-Chen/1996/G2P[4]; AY787652; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: DQ870494; RVA/Vaccine/USA/RotaTeq-SC2-9/1992/G2P7[5]: GU565064; RVA/Vaccine/USA/RotaTeq-WI79-4/1992/G6P1A[8]: GU565042; RVA/Vaccine/USA/RotaTeq-WI79-9/1992/G1P7[5]: GU565053; RVA/Human-tc/USA/DS-1/1976/G2P[4]: HQ650117; RVA/Human-wt/MWI/1473/2001/G8P[4]: HQ657134; RVA/Human-wt/ZAF/3203WC/2009/G2P[4]; HQ657167; RVA/Human-wt/ZAF/GR10924/ 1999/G9P[6]: FJ183354; RVA/Human-wt/USA/LB2744/2006/G2P[4]: HM467931; wt/BGD/RV161/2000/G12P[6]: DQ490546; RVA/Human-wt/DEU/GER1H-09/2009/G8P[4]: GQ414541; RVA/Human-wt/COD/DRC86/2003/G8P[6]: DQ005124; wt/CHN/TB-Chen/1996/G2P[4]: AY787652; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627543; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009630; RVA/Human-tc/ITA/PA169/1988/G6P[14]: EF554127.
170
Genome segment 3 (VP3)
RVA/Cow-wt/JPN/Azuk-1/2006/G21P[29]: AB573081; RVA/Vaccine/USA/RotaTeq-WI78-8/1992/G3P7[5]: GU565076; RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5]: GU565087; RVA/Human-tc/IDN/69M/1980/G8P4[10]: AY277916; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: DQ870495; RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF560617; RVA/Guanaco-wt/ARG/Rio-Negro/1998/G8P[1]: FJ347124; RVA/Cow-tc/GBR/UK/1973/G6P7[5]: AY300923; RVA/Cow-wt/KOR/KJ9-1/XXXX/G6P[7]: HM988964; RVA/Cow-tc/FRA/RF/1982/G6P[1]: AY116592; RVA/Human-tc/USA/Se584/ 1998/G6P[9]: EF583043; VA/Cat-wt/ITA/BA222/2005/G3P[9]: GU827408; RVA/Human-wt/BEL/B1711/2002/G6P[6]: EF554084; RVA/Cow-tc/VEN/BRV033/1990/G6P6[1]: EF560614; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009631; RVA/Human-tc/USA/DS-1/1976/G2P[4]: HQ650118; RVA/Human-wt/MWI/1473/2001/G8P[4]: HQ657135; RVA/Human-wt/ZAF/3203WC/2009/G2P[4]: HQ657168; RVA/Human-wt/ZAF/GR10924/1999/G9P[6]: FJ183355; RVA/Human-wt/CHN/TB-Chen/1996/G2P[4]: AY787654; wt/BGD/MMC88/2005/G2P[4]: HQ641366; RVA/Human-wt/BGD/RV176-00/2000/G12P[6]: DQ490553; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627544.
Genome segment 4 (VP4)
RVA/Cow-wt/THA/61A/XXXX/G10P[5]: D13396; RVA/Pig-wt/THA/P343/XXX/G10P[5]: U35851; RVA/Vaccine/USA/RotaTeq-WI79-9/1992/G1P7[5]: GU565055; RVA/Vaccine/ USA/RotaTeq-WI78-8/1992/G3P7[5]: GU565077; RVA/Human-tc/THA/CJN-M/XXXX/G1P[5]: D16351; RVA/Vaccine/USA/RotaTeq-SC2-9/1992/G2P7[5]: GU565066; RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5]: GU565088; RVA/Cow-tc/FRA/RF/ 1982/G6P[1]: U65924; RVA/Velvet monkey-tc/ZAF/SA11-4F/1958/G3P6[1]: X57319; RVA/Rhesus-tc/USA/PTRV/1990/G8P[1]: FJ422134; RVA/Labstr/USA/SA11g4Oagent/ XXXX/G3P[1]: DQ838602; RVA/Labstr/USA/SA11-30/1A/1958/G3P[1]: DQ838605; RVA/Cow-tc/USA/VMRI/XXXX/G6P[5]: U53923; RVA/Labstr/USA/UKg9D/1984/ G1P[5]: GQ496215; RVA/Labstr/USA/UKg9P/1984/G3P[5]: GQ496246; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009632; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627545; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009631; RVA/Cow-wt/CHN/CHLY/XXXX/G6P[1]: FJ969816; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: AB119636.
171
Genome segment 6 (VP6)
RVA/Cow-tc/USA/WC3/1981/G6P[5]: AF411322; RVA/Cow-wt/KOR/KJ9-1/XXXX/ G6P[7]: HM988974; RVA/Vaccine/USA/RotaTeq-WI78-8/1992/G3P7[5]: GU565078; RVA/Bovine-tc/JPN/22R/XXXX/GXP[X]: AB040055; RVA/Vaccine/USA/RotaTeq-SC2-9/1992/G2P7[5]: GU565067; RVA/Vaccine/USA/RotaTeq-WI79-9/1992/G1P7[5]: GU565056; RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495131; RVA/Cow-tc/USA/ NCDV/1967/G6P6[1]: DQ870496; RVA/Sheep-tc/ESP/OVR762/2002/G8P[14]: EF554152; RVA/Labstr/USA/Rotashield-DS1xRRV/XXXX/G2P[3]: HQ846870: RVA/Cow-tc/CHN/ DQ-75/2008/G10P[11]: GU384194; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: D16329; RVA/Human-wt/COD/DRC88/2003/G8P[8]: DQ005110; RVA/Human-tc/USA/DS-1/1976/G2P[4]: HQ650121; RVA/Human-wt/MWI/1473/2001/G8P[4]: HQ657137; RVA/Human-wt/ZAF/GR10924/1999/G9P[6]: FJ183358; RVA/Human-wt/ZAF/3203WC/ 2009/G2P[4]: HQ657170; RVA/Human-wt/USA/LB2744/2006/G2P[4]: HM467947; RVA/Human-wt/BGD/MMC6/2005/G2P[4]: HQ641358; RVA/Human-wt/CHN/TB-Chen/1996/G2P[4]: AY787645; RVA/Human-tc/JPN/S2/1980/G2P1[4]: DQ870488.
Genome segment 9 (VP7)
RVA/Cow-tc/GBR/UK/1973/G6P7[5]: X00896; RVA/Cow-wt/KOR/KJ69-1/XXXX/G6P[7]: FJ206066; RVA/Foal-wt/IND/Erv99/XXXX/G6P[1]: DQ981478; RVA/Vaccine/USA/ RotaTeq-WI79-4/1992/G6P1A[8]: GU565046; RVA/Human-wt/ITA/PA169/1988/G6P[14]: L20883; RVA/Human-wt/AUS/MG8/1997/G8P[14]: AF207061; RVA/Human-tc/IDN/ 69M/1980/G8P4[10]: EF672560; RVA/Human-wt/GBR/QEH14262/1990/G8P[X]: AF143689; RVA/Human-wt/KEN/B12/1987/G8P[1]: RVA/Cow-wt/CHN/CHLY/XXXX/ G6P[1]: DQ195152; wt/KOR/KV0426/XXXX/G6P[X]: EU873015; RVA/Cow-tc/USA/IND/XXXX/G6P[X]: U15000; RVA/Human-wt/MWI/MW1479/2001/G8P[4]: FJ386441: 85/1985/G8P[X]: RVA/Human-wt/ZAF/GR570-85/1985/G8P[X]: FJ386441; RVA/Human-wt/MW4103/2000/G8P[8]: FJ386443; wt/NGA/HMG035/XXXX/G8P[1]: AF359359; RVA/Human-wt/KEN/1290/1991/G8P[X]: EU488721; RVA/Human-wt/COD/DRC88/2003/G8P[8]: DQ005109: RVA/Human-wt/COD/DRC86/2003/G8P[6]: DQ005120; RVA/Swine-wt/KOR/C-1/2006/G8P[7]: FJ807868; RVA/Human-wt/AUS/WAG8.3/2007/G8P[8][14]: GQ398018; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: D82979.
172
Genome segment 5 (NSP1)
RVA/Human-tc/KEN/B12/1987/G8P[1]: HM627548; RVA/Vaccine/USA/RotaTeq-SC2-9/1992/G2P7[5]: GU565069; RVA/Vaccine/USA/RotaTeq-WI79-4/1992/G6P1A[8]: GU565047; RVA/Vaccine/USA/RotaTeq-WI78-8/1992/G3P7[5]: GU565080; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: GU808570; RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF990699; RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5]: GU565091; RVA/Vaccine/ USA/RotaTeq-WI79-9/1992/G1P7[5]: GU565058; RVA/Human-wt/ITA/111-05-27/2005/G6P[14]: EF554143; RVA/Rhesus-tc/USA/PTRV/1990/G8P[1]: FJ422135; RVA/Cow-wt/THA/A44/1989/G10P[11]: U23726; RVA/giraffe-wt/IRL/UCD/2007/ G10P[11]: GQ428136; RVA/Cow-tc/GBR/UK/1973/G6P7[5]: HQ186289; RVA/Human-wt/BEL/B10925/1997/G6P[14]: EF554121; RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF990699; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009633; RVA/Human-tc/JPN/AU-1/1982/G3P3[9]: D45244; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627548; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: GU808570; RVA/Vaccine/USA/RotaTeq-BrB-9/1996/G4P7[5]: GU565091; RVA/Cow-tc/FRA/RF/1982/G6P[1]: M22308; RVA/Human-wt/ITA/111-05-27/2005/G6P[14]: EF554143.
Genome segment 8 (NSP2)
RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF990700; RVA/Human-wt/JPN/KF17/2010/ G6P[9]: JF421982; RVA/Simian-tc/USA/RRV/1975/G3P[3]: EU636931; RVA/Dog-tc/ITA/RV52-96/1996/G3P[3]: HQ661130; RVA/Human-tc/ITA/PA260-97/1997/G3P[3]: HQ661119; RVA/Simian-tc/USA/RRV/1975/G3P[3]: EU636931; RVA/Cow-tc/CHN/DQ-75/2008/G10P[11]: GU384196; RVA/Rhesus-tc/USA/PTRV/1990/ G8P[1]: FJ422139; RVA/Cow-wt/ARG/B383/1998/G15P[11]: FJ347118; RVA/Sheep-tc/CHN/Lamb-NT/ XXXX/G10P[15]: FJ031020; RVA/Cow-wt/ARG/B383/1998/G15P[11]: FJ347118; RVA/Goat-tc/BGD/GO34/1999/G6P[1]: GU937884; RVA/Labstr/USA/UKg9ST3/1986/ G4P[5]: GQ225816; RVA/Human-wt/KEN/D205/1989/G2P[4]: JF304922; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009625; RVA/Human-wt/COD/DRC86/2003/G8P[6]: DQ005118; tc/IDN/69M/1980/G8P4[10]: EF672559; RVA/Human-wt/MWI/1473/2001/G8P[4]: HQ657140; RVA/Human-wt/ZAF/3203WC/2009/G2P[4]: HQ657173; wt/ZAF/GR10924/1999/G9P[6]: FJ183361; RVA/Human-tc/USA/DS-1/1976/G2P1B[4]: EF672580; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627549; RVA/Cow-tc/GBR/UK/1973/G6P7[5]: J02420.
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Genome segment 7 (NSP3)
RVA/Vaccine/USA/RotaTeq-WI79-9/1992/G1P7[5] NSP3: GU565060; RVA/Vaccine/ USA/RotaTeq-WI78-8/1992/G3P7[5]: GU565082; RVA/Cow-tc/FRA/RF/1982/G6P[1]: Z21639; strain RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF990701; RVA/Human-tc/ITA/PA169/1988/G6P[14]: EF554134; RVA/Sheep-wt/CHN/CC0812-1/2008/G10P[15]: HQ834204; RVA/Human-wt/ITA/PAH136/1996/G3P[9]: GU296415; RVA/Vaccine/USA/ RotaTeq-SC2-9/1992/G2P7[5]: GU565071; RVA/giraffe/UCD/IRL/2007/G10P[11]: GQ428138; wt/ITA/PAI58/1996/G3P[9]: GU296414; RVA/Human-tc/AUS/MG6/1993/G6P[14]: EF554101; RVA/Cow-tc/CHN/DQ-75/2008/G10P[11]: GU384196; RVA/Labstr/USA/UKg9D/1984/G1P[5]: GQ496199; RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495134; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009626; RVA/Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]: FJ347130; RVA/Human-wt/BEL/B10925/1997/G6P[14]: EF554123; RVA/Cow-wt/ARG/B383/1998/G15P[11]: FJ347119; wt/ITA/111-05-27/2005/G6P[14]: EF554145; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627550; RVA/Human-wt/MWI/1473/2001/G8P[4]: HQ657141; RVA/Human-wt/ZAF/3203WC/2009/G2P[4]: HQ657174.
Genome segment 10 (NSP4)
RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627551; RVA/giraffe-wt/IRL/UCD/2007/ G10P[11]: GQ428139; strain RVA/Human-wt/HUN/Hun5/1997/G6P[14]: EF554113; RVA/Human-wt/ITA/111-05-27/2005/G6P[14]: EF554146; RVA/Human-wt/ITA/PAI58/ 1996/G3P[9]: GU296417; RVA/Cat-wt/ITA/BA222/2005/G3P[9]: GU827415; RVA/Human-tc/ITA/PA169/1988/G6P[14]: EF554135; RVA/Human-wt/ITA/PAH136/1996/ G3P[9]: GU296416; wt/COD/DRC88/2003/G8P[8]: DQ005105; RVA/Human-wt/ESP/RV1019/SAG/2009/G8P[6]: RVA/Human-tc/USA/DS-1/1976/G2P[4]: HQ650125; wt/FRA/R1853/2007/G8/P[6]: HM035536; RVA/Human-wt/COD/DRC86/2003/ G8P[6]: DQ005116; RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495135; wt/ESP/RV902/VLC/2008/G8P[6]: HQ674766; RVA/Human-Wt/ITA/PA43/2003/G6P[9]: JF793928; RVA/Human-Wt/THA/CMH134/2005/G2P[4]: GU288649; RVA/Cat-wt/ITA/BA222/2005/G3P[9]: GU827415; RVA/Human-wt/BGD/MMC88/2005/G2P[4]: HQ641371; RVA/Human-wt/USA/LB2764/2006/G2P[4]: HM467980; RVA/Human-wt/ZAF/3203WC/2009/G2P[4]: HQ657175; RVA/Human-wt/ZAF/GR10924/1999/G9P[6]: FJ183363; RVA/Human-wt/MWI/1473/2001/G8P[4]:
174
HQ657142; RVA/Human-wt/CHN/TB-Chen/1996/G2P[4]: AY787650; RVA/Pigeon-tc/JPN/PO-13/1983/G18P[17]: AB009627; RVA/Cow-tc/GBR/UK/1973/G6P7[5]: J02420; RVA/Antelope-wt/ZAF/RC-18-08/G6P[14]: FJ495135.
Genome segment 11 (NSP5)
RVA/Cat-wt/ITA/BA222/2005/G3P[9]: GU827416; RVA/Human-wt/BEL/B10925/1997/ G6P[14]: EF554125; RVA/Goat-tc/BGD/GO34/1999/G6P[1]: GU937887; RVA/Cow-wt/KOR/KJ19-2/XXXX/G6P[7]: FJ206054; RVA/Cow-tc/USA/WC3/1981/G6P[5]: EF990702; RVA/giraffe-wt/IRL/UCD/2007/G10P[11]: RVA/giraffe-wt/ IRL/UCD/2007/ G10P[11]: GQ428140; RVA/Human-wt/ITA/PAH136/1996/G3P[9]: GU296418; RVA/Human-wt/JPN/KF17/2010/G6P[9]: JF421985; RVA/Cow-tc/CHN/DQ-75/2008/ G10P[11]: GU384198; RVA/Cow-wt/ARG/B383/1998/G15P[11]: FJ347121; RVA/ Guanaco-wt/ARG/Rio_Negro/1998/G8P[1]: FJ347132; RVA/Guanaco-wt/ARG/ Chubut/1999/G8P[14]: FJ347110; RVA/Vaccine/USA/RotaTeq-WI79-4/1992/G6P1A[8]: GU565051; tc/ESP/OVR762/2002/G8P[14]: EF554158; RVA/Sheep-wt/CHN/CC0812-1/2008/G10P[15]: HQ834206; RVA/Rhesus-tc/USA/PTRV/1990/G8P[1]: FJ422141; RVA/Human-tc/USA/Se584/1998/G6P[9]: EF672611; RVA/Dog-tc/ITA/RV198-95/1995/G3P[3]: HQ661144; RVA/Human-wt/THA/CMH079/2005/G3P[10]: EU791926; RVA/Cow-tc/USA/NCDV/1967/G6P6[1]: GU937876; RVA/Pigeon-tc/JPN/PO-13/1983/ G18P[17]: AB009628; tc/JPN/AU-1/1982/G3P3[9]: AB008656; RVA/Human-wt/BEL/B10925/1997/G6P[14]: EF554125; RVA/Sheep-tc/CHN/Lamb-NT/XXXX/ G10P[15]: FJ031023; RVA/Human-wt/KEN/B12/1987/G8P[1]: HM627552.
175
Supplement 3. Average sequence coverage for all genome segments of the three bovine
rotaviruses characterised in this study.
Average depth of sequence coverage Genome segment RVA/Cow-wt/ZAF/1603/2007/G6P[5] RVA/Cow-wt/ZAF/1604/2007/G8P[1] RVA/Cow-wt/ZAF/1605/2007/G6P[5] 1 (VP1) 58 147 136 2 (VP2) 124 219 101 3(VP3) 191 317 136 4(VP4) 107 399 114 5 (NSP1) 191 355 151 6 (VP6) 473 374 136 7 (NSP3) 678 210 435 8 (NSP2) 628 399 323 9 (VP7) 499 623 112 10 (NSP4) 182 132 174 11 (NSP5/NSP6) 361 216 142
176
Supplement 4. Size of the complete nucleotide and deduced amino acid sequence of all 11 genome segments of the three study bovine
rotaviruses.
a
NSP1 polypeptide was translated from nt 26 – 967. RVA strains 1603 and 1605 contains nucleotide ‘A’ insertion at position 18.
b
NSP3 polypeptide for RVA strains 1603 and 1605 was translated from nt 32 – 1507, whereas NSP3 polypeptide for RVA strains 1604 was translated from nt 33 – 1508. RVA strains 1603 and 1605 contains nucleotides ‘GACT’ insertions from position 983 – 986.
Study bovine rotavirus strains Genome segments Nucleotides (nt) S9(VP7) S4(VP4) S6(VP6) S1(VP1) S2(VP2) S3(VP3) S5(NSP1) S8(NSP2) S7(NSP3) S10(NSP4) S11(NSP5) RVA/Cow-wt/ZAF/1603/2007/G6P[5] 1062 2362 1356 3302 2687 2591 1579a 1059 1074b 751 667 RVA/Cow-wt/ZAF/1604/2007/G8P[1] 1062 2362 1356 3302 2687 2591 1578 1059 1078 751 667 RVA/Cow-wt/ZAF/1605/2007/G6P[5] 1062 2362 1356 3302 2687 2591 1579 a 1059 1074 b 751 667
Deduced amino acids (aa)
(VP7)S9 (VP4)S4 (VP6)S6 (VP1)S1 (VP2)S2 (VP3)S3 (NSP1)S5 (NSP2)S8 (NSP3)S7 (NSP4)S10 (NSP5)S11 RVA/Cow-wt/ZAF/1603/2007/G6P[5] 326 776 397 1088 880 835 491 317 313 175 198 RVA/Cow-wt/ZAF/1604/2007/G8P[1] 326 776 397 1088 880 835 491 317 313 175 198 RVA/Cow-wt/ZAF/1605/2007/G6P[5] 326 776 397 1088 880 835 491 317 313 175 198
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Supplement 5. Phylogenetic trees based on the full-length consensus nucleotide sequence of
rotavirus genome segments 1–11 encoding structural (VP1–VP4, VP6 and VP7) and non-structural (NSP1–NSP5) proteins. The nomenclature of all the rotavirus strains included in the trees indicate the rotavirus group/species of origin-(wild type or tissue culture sample)/country of identification (unique 3-letter abbreviation code for each country)/common name of the sample/year of isolation/G- and P-type of each strain as proposed by the RCWG (Matthijnssens et al., 2011). Accession numbers of all the nucleotide sequences of the strains used for comparison in the phylogenetic trees are listed in Supplement 2. The study strains are marked with a black diamond. The horizontal branch lengths are proportional to the genetic distance calculated by the Neighbour-Joining method. The numbers adjacent to the nodes represent the bootstrap value of 1,000 replicates, and values less than 70% were not shown. The scale bars represent nucleotide substitutions per site.
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Supplement 6. Distance matrices. A. Genome segment 1 (VP1)
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K. Genome segment 11 (NSP5)
Supplement 6. Estimates of the evolutionary divergence between the nucleotide sequences of 11 genome segments (1–11) of the study bovine rotaviruses compared to some closely related sequences acquired from the GenBank. The accession numbers of all the nucleotide sequences of the strains used for comparison are listed in Supplement 2. The number of base substitutions per site from analysis between sequences is shown as a variance estimated by a bootstrap approach. All results are based on the pairwise analysis of the number of sequences compared for each genome segment. Analyses were conducted using the Maximum Composite Likelihood method in MEGA4 (Tamura et al., 2007). Codon positions included were 1st+2nd+3rd+non-coding. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). The variances between the three study samples are boxed. The complete nomenclature for each strain is listed in Supplement 2.
